[ensembl-dev] Question on Ensembl IDs from StringDB

[Sam Altshuler]

Hi, 

I am working on creating a Protein Protein Interaction Network for my lab
and I am attempting to convert from String ID to the gene name.

I found this as a possible answer for how to convert the two ID forms
(https://www.biostars.org/p/342160/), but since I am using Neurospora Crassa
and not Human models, I had to modify it a bit. This is the code that I
used:

library("biomaRt")

listMarts(host = "https://fungi.ensembl.org", port = 443)

test <- c("EFNCRP00000000466", "EFNCRP00000000314", "EFNCRP00000000407",
"EFNCRP00000000083")

ensembl_fungi <- useMart(host="https://fungi.ensembl.org", 

                         biomart="fungi_mart", 

                         port = 443,

                         dataset =  "ncrassa_eg_gene")

 

conversion.table <- data.frame(getBM(attributes =
c("ensembl_gene_id","ensembl_peptide_id", "uniprotswissprot",
"uniprotsptrembl"),

                                     filters = "ensembl_peptide_id",

                            values = list(test),

                            mart = ensembl_fungi))

head(conversion.table)

This results in an empty data frame. When I put the gene ID's for each of
these (previously known) in as the test and filter by "ensembl_gene_id", it
says the peptide IDs are: EAA26917, EAA26918, EAA28465, EAA28503, which is
very different than what String says the ensembl peptide IDs should be.

Does anyone know why this is happening or how to convert from StringID to a
gene name directly?

 

 

Sam Altshuler 

RPI Class of 2021 

Bioinformatics and Molecular Biology 

 <mailto:Altshs at rpi.edu> Altshs at rpi.edu | 651-558-6327

 

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